[{"month":"09","publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"supervisor":[{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:14280","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"name":"Reconstitution of bacterial cell wall sythesis","_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2023-10-04T10:28:35Z","ec_funded":1,"date_updated":"2024-02-21T12:35:18Z","date_created":"2023-09-06T10:58:25Z","author":[{"full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp"}],"related_material":{"record":[{"id":"11373","status":"public","relation":"part_of_dissertation"},{"id":"7387","status":"public","relation":"part_of_dissertation"},{"relation":"research_data","status":"public","id":"10934"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"year":"2023","day":"25","has_accepted_license":"1","article_processing_charge":"No","keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"date_published":"2023-09-25T00:00:00Z","page":"156","citation":{"mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280"},"abstract":[{"text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"checksum":"87eef11fbc5c7df0826f12a3a629b444","date_updated":"2023-10-04T10:28:35Z","date_created":"2023-10-04T10:11:53Z","relation":"source_file","file_id":"14390","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":114932847,"creator":"pradler","access_level":"closed","file_name":"PhD Thesis_Philipp Radler_20231004.docx"},{"embargo_to":"open_access","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","access_level":"closed","content_type":"application/pdf","file_size":37838778,"creator":"pradler","relation":"main_file","file_id":"14391","embargo":"2024-10-04","date_updated":"2023-10-04T10:28:35Z","date_created":"2023-10-04T10:11:21Z","checksum":"3253e099b7126469d941fd9419d68b4f"}],"ddc":["572"],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","status":"public","_id":"14280","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2023-08-11T14:39:17Z","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","date_created":"2023-07-24T14:10:45Z","date_updated":"2024-02-21T12:35:34Z","related_material":{"record":[{"id":"13312","relation":"part_of_dissertation","status":"public"},{"id":"12118","status":"public","relation":"part_of_dissertation"},{"id":"8910","relation":"part_of_dissertation","status":"public"},{"id":"12522","relation":"research_data","status":"public"}]},"author":[{"last_name":"Valentini","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","full_name":"Valentini, Marco"}],"publication_identifier":{"issn":["2663 - 337X"]},"month":"07","project":[{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e","grant_number":"F8606","name":"Conventional and unconventional topological superconductors"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"language":[{"iso":"eng"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"supervisor":[{"orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios"}],"doi":"10.15479/at:ista:13286","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices."}],"title":"Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium","ddc":["530"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"13286","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"14033","date_created":"2023-08-11T09:27:39Z","date_updated":"2023-08-11T10:01:34Z","checksum":"666ee31c7eade89679806287c062fa14","file_name":"PhD_thesis_Valentini_final.zip","access_level":"closed","content_type":"application/x-zip-compressed","file_size":56121429,"creator":"mvalenti"},{"file_id":"14035","relation":"main_file","checksum":"0992f2ebef152dee8e70055350ebbb55","date_updated":"2023-08-11T14:39:17Z","date_created":"2023-08-11T14:39:17Z","access_level":"open_access","file_name":"PhD_thesis_Valentini_final_validated.pdf","creator":"mvalenti","file_size":38199711,"content_type":"application/pdf"}],"article_processing_charge":"No","has_accepted_license":"1","day":"21","page":"184","citation":{"chicago":"Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.","short":"M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.","mla":"Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.","apa":"Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286","ieee":"M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.","ista":"Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.","ama":"Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286"},"date_published":"2023-07-21T00:00:00Z"},{"doi":"10.15479/at:ista:13984","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"supervisor":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-034-3"]},"month":"08","year":"2023","department":[{"_id":"GradSch"},{"_id":"SyCr"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"last_name":"Franschitz","first_name":"Anna","id":"480826C8-F248-11E8-B48F-1D18A9856A87","full_name":"Franschitz, Anna"}],"date_updated":"2024-03-01T15:25:17Z","date_created":"2023-08-08T15:33:29Z","file_date_updated":"2024-03-01T12:58:14Z","citation":{"chicago":"Franschitz, Anna. “Individual and Social Immunity against Viral Infections in Ants.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13984.","short":"A. Franschitz, Individual and Social Immunity against Viral Infections in Ants, Institute of Science and Technology Austria, 2023.","mla":"Franschitz, Anna. Individual and Social Immunity against Viral Infections in Ants. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13984.","ieee":"A. Franschitz, “Individual and social immunity against viral infections in ants,” Institute of Science and Technology Austria, 2023.","apa":"Franschitz, A. (2023). Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13984","ista":"Franschitz A. 2023. Individual and social immunity against viral infections in ants. Institute of Science and Technology Austria.","ama":"Franschitz A. Individual and social immunity against viral infections in ants. 2023. doi:10.15479/at:ista:13984"},"page":"89","date_published":"2023-08-08T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"08","_id":"13984","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Individual and social immunity against viral infections in ants","ddc":["570","577"],"status":"public","file":[{"relation":"main_file","file_id":"13986","embargo":"2024-08-08","date_updated":"2024-03-01T08:51:42Z","date_created":"2023-08-08T18:01:28Z","checksum":"27220243d5d51c3b0d7d61c0879d7a0c","embargo_to":"open_access","file_name":"Thesis_AnnaFranschitz_202308.pdf","access_level":"closed","file_size":10797612,"content_type":"application/pdf","creator":"afransch"},{"file_name":"Thesis_AnnaFranschitz_202308.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":2619085,"creator":"afransch","relation":"source_file","file_id":"13987","date_created":"2023-08-08T18:02:25Z","date_updated":"2023-08-09T07:25:27Z","checksum":"40abf7ccca14a3893f72dc7fb88585d6"},{"content_type":"application/pdf","file_size":85956,"creator":"cchlebak","access_level":"closed","embargo_to":"open_access","description":"Minor modifications and clarifications - Feb 2024","file_name":"Addendum_AnnaFranschitz202402.pdf","checksum":"8b991ecc2d59d045cc3cf0d676785ec7","date_updated":"2024-03-01T12:13:29Z","date_created":"2024-03-01T08:37:15Z","relation":"erratum","title":"Addendum","file_id":"15042","embargo":"2024-08-08"},{"checksum":"66745aa01f960f17472c024875c049ed","date_created":"2024-03-01T08:39:20Z","date_updated":"2024-03-01T08:51:42Z","relation":"source_file","file_id":"15043","title":"Addendum - source file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":11818,"creator":"cchlebak","access_level":"closed","file_name":"Addendum_AnnaFranschitz202402.docx"},{"creator":"cchlebak","file_size":10416761,"content_type":"application/pdf","file_name":"Print_Version_Franschitz_Anna_Thesis.pdf","description":"For printing purposes","access_level":"closed","date_updated":"2024-03-01T12:58:14Z","date_created":"2024-03-01T08:56:06Z","checksum":"55c876b73d49db15228a7f571592ec77","title":"Print Version","file_id":"15044","relation":"other"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"Social insects fight disease using their individual immune systems and the cooperative\r\nsanitary behaviors of colony members. These social defenses are well explored against\r\nexternally-infecting pathogens, but little is known about defense strategies against\r\ninternally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades\r\nit has become evident that also many ant species harbor viruses. We present one of the first\r\nstudies addressing transmission dynamics and collective disease defenses against viruses in\r\nants on a mechanistic level. I successfully established an experimental ant host – viral\r\npathogen system as a model for the defense strategies used by social insects against internal\r\npathogen infections, as outlined in the third chapter. In particular, we studied how garden ants\r\n(Lasius neglectus) defend themselves and their colonies against the generalist insect virus\r\nCrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’\r\nhemolymph because it allowed us to use a defined exposure dose. Here we show that this is a\r\ngood model system, as the virus is replicating and thus infecting the host. The ants mount a\r\nclear individual immune response against the viral infection, which is characterized by a\r\nspecific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21\r\nand 22 bp long fragments. The onset of this immune response is consistent with the timeline\r\nof viral replication that starts already within two days post injection. The disease manifests in\r\ndecreased survival over a course of two to three weeks.\r\nRegarding group living, we find that infected ants show a strong individual immune response,\r\nbut that their course of disease is little affected by nestmate presence, as described in chapter\r\nfour. Hence, we do not find social immunity in the context of viral infections in ants.\r\nNestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we\r\nshowed that 94 % of the nestmates contract active virus within four days of social contact to\r\nan infected individual. Virus is transmitted in low doses, thus not causing disease\r\ntransmission within the colony. While virus can be transmitted during short direct contacts,\r\nwe also assume transmission from deceased ants and show that the nestmates’ immune\r\nsystem gets activated after contracting a low viral dose. We find considerable potential for\r\nindirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one\r\nweek and is also picked up by other ants. Apart from that, we want to underline the potential\r\nof ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV\r\nin vitro. However, we found no evidence for effective poison use to sanitize the nest space.\r\nOn the other hand, local application of ant poison by oral poison uptake, which is part of the\r\nants prophylactic behavioral repertoire, probably contributes to keeping the gut of each\r\nindividual sanitized. We hypothesize that oral poison uptake might be the reason why we did\r\nnot find viable virus in the trophallactic fluid.\r\nThe fifth chapter encompasses preliminary data on potential social immunization. However,\r\nour experiments do not confirm an actual survival benefit for the nestmates upon pathogen\r\nchallenge under the given experimental settings. Nevertheless, we do not want to rule out the\r\npossibility for nestmate immunization, but rather emphasize that considering different\r\nexperimental timelines and viral doses would provide a multitude of options for follow-up\r\nexperiments.\r\nIn conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,\r\nmight play a role in preventing viral disease transmission. Compared to colony defense\r\nagainst external pathogens, internal pathogen infections require a stronger component of\r\nindividual physiological immunity than behavioral social immunity, yet could still lead to\r\ncollective protection."}]},{"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","supervisor":[{"first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"doi":"10.15479/at:ista:14323","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"publication_identifier":{"issn":["2663 - 337X"]},"month":"09","date_created":"2023-09-13T10:07:18Z","date_updated":"2024-03-07T15:02:59Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7883"}]},"author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87","first_name":"Katarzyna","last_name":"Kuzmicz-Kowalska"}],"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2023","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2023-09-13T10:08:25Z","date_published":"2023-09-13T00:00:00Z","page":"151","citation":{"ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","apa":"Kuzmicz-Kowalska, K. (2023). Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14323","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023.","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:10.15479/at:ista:14323","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14323.","mla":"Kuzmicz-Kowalska, Katarzyna. Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14323.","short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023."},"has_accepted_license":"1","article_processing_charge":"No","day":"13","oa_version":"Published Version","file":[{"checksum":"bd83596869c814b24aeff7077d031c0e","date_updated":"2023-09-13T10:08:25Z","date_created":"2023-09-13T09:52:52Z","file_id":"14324","embargo":"2025-03-13","relation":"main_file","creator":"kkuzmicz","file_size":10147911,"content_type":"application/pdf","access_level":"closed","file_name":"PhDThesis_KK_final_pdfA.pdf","embargo_to":"open_access"},{"file_id":"14325","relation":"source_file","checksum":"aa2757ae4c3478041fd7e62c587d3e4d","date_created":"2023-09-13T09:53:29Z","date_updated":"2023-09-13T09:53:29Z","access_level":"closed","file_name":"thesis_KK_final_corrections_092023.docx","creator":"kkuzmicz","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":103980668}],"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","status":"public","ddc":["570"],"_id":"14323","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"month":"11","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:14641","degree_awarded":"PhD","supervisor":[{"full_name":"Hof, Björn","last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2024-03-20T13:19:36Z","ec_funded":1,"author":[{"first_name":"Mike","last_name":"Hennessey-Wesen","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike"}],"date_updated":"2024-03-22T13:21:17Z","date_created":"2023-12-04T13:17:37Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"publisher":"Institute of Science and Technology Austria","day":"30","has_accepted_license":"1","article_processing_charge":"No","keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"date_published":"2023-11-30T00:00:00Z","citation":{"ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023.","apa":"Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641.","mla":"Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641.","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023."},"page":"104","type":"dissertation","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","file":[{"relation":"source_file","file_id":"14648","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","date_updated":"2023-12-06T13:13:26Z","date_created":"2023-12-06T13:13:26Z","access_level":"closed","file_name":"mike_thesis_v06-12-2023.odt","content_type":"application/vnd.oasis.opendocument.text","file_size":46405919,"creator":"mhenness"},{"creator":"mhenness","content_type":"application/pdf","file_size":21282155,"access_level":"closed","file_name":"mike_thesis_v06-12-2023.pdf","embargo_to":"open_access","checksum":"f5203a61eddaf35235bbc51904d73982","date_updated":"2023-12-06T13:14:15Z","date_created":"2023-12-06T13:14:15Z","embargo":"2024-11-30","file_id":"14649","relation":"main_file"},{"file_id":"15145","relation":"other","date_created":"2024-03-20T13:19:36Z","date_updated":"2024-03-20T13:19:36Z","checksum":"9f7b4d646f1cfb57e3b9106a8a9cdd9d","file_name":"2023_Hennessey_Michael_Thesis_from_source.pdf","access_level":"closed","creator":"cchlebak","content_type":"application/pdf","file_size":2930287}],"_id":"14641","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["570"],"status":"public","title":"Adaptive mutation in E. coli modulated by luxS"},{"file_date_updated":"2024-03-20T12:28:32Z","ec_funded":1,"year":"2023","acknowledgement":"The research projects contained in this thesis have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819).","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JuFi"}],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Alice","last_name":"Marveggio","id":"25647992-AA84-11E9-9D75-8427E6697425","full_name":"Marveggio, Alice"}],"related_material":{"record":[{"id":"11842","relation":"part_of_dissertation","status":"public"},{"id":"14597","status":"public","relation":"part_of_dissertation"}]},"date_created":"2023-11-21T11:41:05Z","date_updated":"2024-03-22T13:21:28Z","month":"11","publication_identifier":{"issn":["2663 - 337X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"project":[{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819"}],"doi":"10.15479/at:ista:14587","degree_awarded":"PhD","supervisor":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"}],"language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"This thesis concerns the application of variational methods to the study of evolution problems arising in fluid mechanics and in material sciences. The main focus is on weak-strong stability properties of some curvature driven interface evolution problems, such as the two-phase Navier–Stokes flow with surface tension and multiphase mean curvature flow, and on the phase-field approximation of the latter. Furthermore, we discuss a variational approach to the study of a class of doubly nonlinear wave equations.\r\nFirst, we consider the two-phase Navier–Stokes flow with surface tension within a bounded domain. The two fluids are immiscible and separated by a sharp interface, which intersects the boundary of the domain at a constant contact angle of ninety degree. We devise a suitable concept of varifolds solutions for the associated interface evolution problem and we establish a weak-strong uniqueness principle in case of a two dimensional ambient space. In order to focus on the boundary effects and on the singular geometry of the evolving domains, we work for simplicity in the regime of same viscosities for the two fluids.\r\nThe core of the thesis consists in the rigorous proof of the convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow for a suitable class of multi- well potentials and for well-prepared initial data. We even establish a rate of convergence. Our relative energy approach relies on the concept of gradient-flow calibration for branching singularities in multiphase mean curvature flow and thus enables us to overcome the limitations of other approaches. To the best of the author’s knowledge, our result is the first quantitative and unconditional one available in the literature for the vectorial/multiphase setting.\r\nThis thesis also contains a first study of weak-strong stability for planar multiphase mean curvature flow beyond the singularity resulting from a topology change. Previous weak-strong results are indeed limited to time horizons before the first topology change of the strong solution. We consider circular topology changes and we prove weak-strong stability for BV solutions to planar multiphase mean curvature flow beyond the associated singular times by dynamically adapting the strong solutions to the weak one by means of a space-time shift.\r\nIn the context of interface evolution problems, our proofs for the main results of this thesis are based on the relative energy technique, relying on novel suitable notions of relative energy functionals, which in particular measure the interface error. Our statements follow from the resulting stability estimates for the relative energy associated to the problem.\r\nAt last, we introduce a variational approach to the study of nonlinear evolution problems. This approach hinges on the minimization of a parameter dependent family of convex functionals over entire trajectories, known as Weighted Inertia-Dissipation-Energy (WIDE) functionals. We consider a class of doubly nonlinear wave equations and establish the convergence, up to subsequences, of the associated WIDE minimizers to a solution of the target problem as the parameter goes to zero."}],"_id":"14587","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences","status":"public","ddc":["515"],"file":[{"content_type":"application/pdf","file_size":2881100,"creator":"amarvegg","file_name":"thesis_Marveggio.pdf","access_level":"open_access","date_updated":"2023-11-29T09:09:31Z","date_created":"2023-11-29T09:09:31Z","checksum":"6c7db4cc86da6cdc79f7f358dc7755d4","success":1,"relation":"main_file","file_id":"14626"},{"relation":"source_file","file_id":"14627","checksum":"52f28bdf95ec82cff39f3685f9c48e7d","date_updated":"2024-03-20T12:28:32Z","date_created":"2023-11-29T09:10:19Z","access_level":"closed","file_name":"Thesis_Marveggio.zip","file_size":10189696,"content_type":"application/zip","creator":"amarvegg"}],"oa_version":"Published Version","day":"21","article_processing_charge":"No","has_accepted_license":"1","citation":{"ama":"Marveggio A. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. 2023. doi:10.15479/at:ista:14587","apa":"Marveggio, A. (2023). Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14587","ieee":"A. Marveggio, “Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences,” Institute of Science and Technology Austria, 2023.","ista":"Marveggio A. 2023. Weak-strong stability and phase-field approximation of interface evolution problems in fluid mechanics and in material sciences. Institute of Science and Technology Austria.","short":"A. Marveggio, Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences, Institute of Science and Technology Austria, 2023.","mla":"Marveggio, Alice. Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14587.","chicago":"Marveggio, Alice. “Weak-Strong Stability and Phase-Field Approximation of Interface Evolution Problems in Fluid Mechanics and in Material Sciences.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14587."},"page":"228","date_published":"2023-11-21T00:00:00Z"},{"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","year":"2023","date_created":"2023-02-02T14:50:20Z","date_updated":"2024-03-25T23:30:05Z","author":[{"first_name":"Bettina","last_name":"Zens","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9561-1239","full_name":"Zens, Bettina"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8586"}]},"file_date_updated":"2024-02-08T23:30:04Z","project":[{"name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions","_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"oa":1,"supervisor":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","full_name":"Schur, Florian KM"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12491","month":"02","publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"ddc":["570"],"status":"public","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12491","oa_version":"Published Version","file":[{"file_name":"PhDThesis_BettinaZens_2023_final.pdf","access_level":"open_access","file_size":23082464,"content_type":"application/pdf","creator":"bzens","relation":"main_file","embargo":"2024-02-07","file_id":"12527","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:07:38Z","checksum":"069d87f025e0799bf9e3c375664264f2"},{"relation":"source_file","file_id":"12528","date_updated":"2024-02-08T23:30:04Z","date_created":"2023-02-07T13:09:05Z","checksum":"8c66ed203495d6e078ed1002a866520c","embargo_to":"open_access","file_name":"PhDThesis_BettinaZens_2023_final.docx","access_level":"closed","file_size":106169509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"bzens"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.","lang":"eng"}],"page":"187","citation":{"ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491."},"date_published":"2023-02-02T00:00:00Z","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"day":"02","article_processing_charge":"No","has_accepted_license":"1"},{"article_processing_charge":"No","has_accepted_license":"1","day":"24","page":"43","citation":{"chicago":"Stephenson, Elizabeth R. “Generalizing Medial Axes with Homology Switches.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14226.","short":"E.R. Stephenson, Generalizing Medial Axes with Homology Switches, Institute of Science and Technology Austria, 2023.","mla":"Stephenson, Elizabeth R. Generalizing Medial Axes with Homology Switches. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14226.","apa":"Stephenson, E. R. (2023). Generalizing medial axes with homology switches. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14226","ieee":"E. R. Stephenson, “Generalizing medial axes with homology switches,” Institute of Science and Technology Austria, 2023.","ista":"Stephenson ER. 2023. Generalizing medial axes with homology switches. Institute of Science and Technology Austria.","ama":"Stephenson ER. Generalizing medial axes with homology switches. 2023. doi:10.15479/at:ista:14226"},"date_published":"2023-08-24T00:00:00Z","alternative_title":["ISTA Master's Thesis"],"type":"dissertation","abstract":[{"text":"We introduce the notion of a Faustian interchange in a 1-parameter family of smooth\r\nfunctions to generalize the medial axis to critical points of index larger than 0.\r\nWe construct and implement a general purpose algorithm for approximating such\r\ngeneralized medial axes.","lang":"eng"}],"ddc":["500"],"title":"Generalizing medial axes with homology switches","status":"public","_id":"14226","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","file":[{"date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:02:49Z","checksum":"453caf851d75c3478c10ed09bd242a91","relation":"source_file","file_id":"14227","content_type":"application/x-zip-compressed","file_size":15501411,"creator":"cchlebak","embargo_to":"open_access","file_name":"documents-export-2023-08-24.zip","access_level":"closed"},{"date_updated":"2024-02-26T23:30:03Z","date_created":"2023-08-24T13:03:42Z","checksum":"7349d29963d6695e555e171748648d9a","relation":"main_file","embargo":"2024-02-25","file_id":"14228","content_type":"application/pdf","file_size":6854783,"creator":"cchlebak","file_name":"thesis_pdf_a.pdf","access_level":"open_access"}],"publication_identifier":{"issn":["2791-4585"]},"month":"08","oa":1,"language":[{"iso":"eng"}],"degree_awarded":"MS","supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"doi":"10.15479/at:ista:14226","file_date_updated":"2024-02-26T23:30:03Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publication_status":"published","year":"2023","date_updated":"2024-02-26T23:30:04Z","date_created":"2023-08-24T13:01:18Z","author":[{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","last_name":"Stephenson","full_name":"Stephenson, Elizabeth R"}]},{"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"20230109_PhD_thesis_JM_final.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":41771714,"embargo":"2023-07-09","file_id":"12471","relation":"main_file","checksum":"1a2306e5f59f52df598e7ecfadf921ac","date_updated":"2023-07-27T22:30:54Z","date_created":"2023-01-31T15:11:42Z"},{"relation":"source_file","file_id":"12472","checksum":"0bebbdee0773443959e1f6ab8caf281f","date_updated":"2023-07-10T22:30:04Z","date_created":"2023-01-31T15:11:51Z","access_level":"closed","embargo_to":"open_access","file_name":"20230109_PhD_thesis_JM_final.docx","file_size":66983464,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"cchlebak"}],"title":"A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy","ddc":["610"],"status":"public","_id":"12470","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of \r\nconnections that orchestrate our cognition and behavior. To decode its complex connectivity, it is \r\npivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of \r\nnm-small synapses.\r\nTo achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across \r\nScales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (super\u0002resolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular\r\nspace, that is compatible with chemical fixation, with information on molecular markers, super\u0002resolved data acquisition and machine-learning based data analysis for segmentation and synapse \r\nidentification.\r\nI used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue \r\narchitecture, neuronal in- and output-fields, down to synapse morphology.\r\nFocusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy \r\nfiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 \r\npyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal \r\nconnectivity with light microscopy.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-01-09T00:00:00Z","page":"201","citation":{"ama":"Michalska JM. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. 2023. doi:10.15479/at:ista:12470","apa":"Michalska, J. M. (2023). A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12470","ieee":"J. M. Michalska, “A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy,” Institute of Science and Technology Austria, 2023.","ista":"Michalska JM. 2023. A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy. Institute of Science and Technology Austria.","short":"J.M. Michalska, A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy, Institute of Science and Technology Austria, 2023.","mla":"Michalska, Julia M. A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12470.","chicago":"Michalska, Julia M. “A Versatile Toolbox for the Comprehensive Analysis of Nervous Tissue Organization with Light Microscopy.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12470."},"day":"09","article_processing_charge":"No","has_accepted_license":"1","date_created":"2023-01-31T15:10:53Z","date_updated":"2023-08-31T12:26:58Z","author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","first_name":"Julia M","last_name":"Michalska","full_name":"Michalska, Julia M"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11943"},{"relation":"part_of_dissertation","status":"public","id":"11950"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"publisher":"Institute of Science and Technology Austria","year":"2023","file_date_updated":"2023-07-27T22:30:54Z","ec_funded":1,"supervisor":[{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12470","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"01","publication_identifier":{"issn":["2663-337X"],"isbn":[" 978-3-99078-026-8"]}},{"has_accepted_license":"1","article_processing_charge":"No","day":"08","date_published":"2023-02-08T00:00:00Z","citation":{"ama":"Kirillova K. Panoramic functional gradients across the mouse retina. 2023. doi:10.15479/at:ista:12531","ieee":"K. Kirillova, “Panoramic functional gradients across the mouse retina,” Institute of Science and Technology Austria, 2023.","apa":"Kirillova, K. (2023). Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12531","ista":"Kirillova K. 2023. Panoramic functional gradients across the mouse retina. Institute of Science and Technology Austria.","short":"K. Kirillova, Panoramic Functional Gradients across the Mouse Retina, Institute of Science and Technology Austria, 2023.","mla":"Kirillova, Kseniia. Panoramic Functional Gradients across the Mouse Retina. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12531.","chicago":"Kirillova, Kseniia. “Panoramic Functional Gradients across the Mouse Retina.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12531."},"page":"46","abstract":[{"text":"All visual experiences of the vertebrates begin with light being converted into electrical signals\r\nby the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the\r\nmammal retina, and they transmit visual information to the rest of the brain.\r\nIt has been shown that RGCs vary in their morphology and genetic profiles, moreover they can\r\nbe unambiguously grouped into subtypes that share the same morphological and/or molecular\r\nproperties. However, in terms of RGCs function, it remains unclear how many distinct types\r\nthere are and what response properties their typology relies on. Even given the recent studies\r\nthat successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the\r\nquestion remains whether the found subtypes persist across the entire retina.\r\nIn this work, using a novel imaging method, we show that, when sampled from a large portion\r\nof the retina, RGCs can not be clearly divided into functional subtypes. We found that in\r\nphotopic conditions, which implies more prominent natural scene statistic differences across\r\nthe visual field, response properties can be exhibited by cells differently depending on their\r\nlocation in the retina, which leads to formation of a gradient of features rather than distinct\r\nclasses.\r\nThis finding suggests that RGCs follow a global organization across the visual field of the\r\nanimal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":8369317,"creator":"cchlebak","access_level":"open_access","file_name":"Thesis_Kseniia___ISTA__istaustriathesis_PDF-A.pdf","checksum":"57d8da3a6c749eb1556b7435fe266a5f","date_updated":"2024-02-09T23:30:03Z","date_created":"2023-02-09T08:03:32Z","relation":"main_file","file_id":"12532","embargo":"2024-02-08"},{"file_id":"12535","relation":"source_file","date_updated":"2024-02-09T23:30:03Z","date_created":"2023-02-10T09:32:06Z","checksum":"87fb44318e4f9eb9da2ad9ad6ca8e76f","file_name":"Thesis Kseniia - ISTA [istaustriathesis]-FINAL.zip","embargo_to":"open_access","access_level":"closed","creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":11204408}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12531","title":"Panoramic functional gradients across the mouse retina","status":"public","ddc":["570"],"publication_identifier":{"issn":["2791-4585"]},"month":"02","doi":"10.15479/at:ista:12531","language":[{"iso":"eng"}],"supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"degree_awarded":"MS","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"file_date_updated":"2024-02-09T23:30:03Z","author":[{"id":"8e3f931e-dc85-11ea-9058-e7b957bf23f0","first_name":"Kseniia","last_name":"Kirillova","full_name":"Kirillova, Kseniia"}],"date_updated":"2024-02-09T23:30:04Z","date_created":"2023-02-09T07:45:05Z","year":"2023","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published"}]